[gmx-users] position restraints

[abdullah ahmed]

Hi,

Sorry to bother you again, but I am new to gromacs and many theings don't make sense yet. 
I have tried reading the manual but I do not understand what you mean by "Note how the automatically-generated "posre.itp" file is #included at 
the end of the Protein_A moleculetype, *before* any other 
molecules are introduced. You have to do the same with any new #include statements or 
directives you add." 

I tried using #include in front of my code for [position_restraints] but that just gives an error. So I suppose that isn't what you mean. 
Furthermore, in section 5.7.1 of the manual pg110 an example topology file called urea.top is shown. there is no include there.

In this example .top file they just seem to have added the position restraints they want after the dihedrals. This approach does not seem to be working for me and I can not understand why. 

Thank you again for your help, 
Abdullah

> Date: Thu, 3 Jun 2010 09:43:18 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] position restraints
> 
> 
> 
> abdullah ahmed wrote:
> > Hi!
> > 
> > In your previous mail you mentioned:
> > 
> > The position restraints must belong to the [moleculetype] of
> > the species to be restrained. * Once you #include a new molecule, you 
> > start a new
> > [moleculetype] entry and the position restraints belong to it. *
> >  
> > 
> > So I rechecked my .top file and found that [moleculetype] only occurs 
> > once. Perhaps I have misunderstood you. So I added the top file below. I 
> 
> No it doesn't.  Each time you #include a new .itp file, you are telling grompp 
> to copy and paste the contents of that .itp file in that location.  Have a look 
> at spc.itp - it starts a new moleculetype.
> 
> http://www.gromacs.org/Documentation/Include_File_Mechanism
> 
> Note how the automatically-generated "posre.itp" file is #included at the end of 
> the Protein_A moleculetype, *before* any other molecules are introduced.  You 
> have to do the same with any new #include statements or directives you add.
> 
> -Justin
> 
> > did not add the contents of [atoms] [bonds] etc because I felt the mail 
> > would become unnecessarily long.
> > 
> > ; Include forcefield parameters
> > #include "ffoplsaa.itp"
> > 
> > [ moleculetype ]
> > ; Name            nrexcl
> > Protein_A           3
> > 
> > [ atoms ]
> > 
> > [ bonds ]
> > 
> > [ pairs ]
> > 
> > [ angles ]
> > 
> > [ dihedrals ]
> > 
> > [ dihedrals ]
> > 
> > ; Include Position restraint file
> > #ifdef POSRES
> > #include "posre.itp"
> > #endif
> > 
> > ; Include water topology
> > #include "spc.itp"
> > 
> > #ifdef POSRES_WATER
> > ; Position restraint for each water oxygen
> > [ position_restraints ]
> > ;  i funct       fcx        fcy        fcz
> >    1    1       1000       1000       1000
> > #endif
> > 
> > ; Include generic topology for ions
> > #include "ions.itp"
> > 
> > [ system ]
> > ; Name
> > Protein
> > 
> > [ molecules ]
> > ; Compound        #mols
> > Protein_A           1
> > 
> > Thanks again for your help,
> > Abdullah
> > 
> > 
> > ------------------------------------------------------------------------
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> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
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